From: Pierre Neidhardt <mail@ambrevar.xyz>
To: 35792@debbugs.gnu.org
Subject: [bug#35792] [PATCH 2/7] gnu: Add smithwaterman.
Date: Sat, 18 May 2019 19:26:35 +0200 [thread overview]
Message-ID: <20190518172640.7165-2-mail@ambrevar.xyz> (raw)
In-Reply-To: <20190518172640.7165-1-mail@ambrevar.xyz>
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 244741854d..1bf33853b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14869,3 +14869,33 @@ might be caused by ATAC-seq library prep or sequencing. The main program,
(description "This is a C++ wrapper around the Tabix project which abstracts
some of the details of opening and jumping in tabix-indexed files.")
(license license:expat)))
+
+(define-public smithwaterman
+ ;; TODO: Upgrading smithwaterman breaks FreeBayes.
+ (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
+ (package
+ (name "smithwaterman")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/smithwaterman/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "smithwaterman" bin)))))))
+ (home-page "https://github.com/ekg/smithwaterman")
+ (synopsis "Implementation of the Smith-Waterman algorithm")
+ (description "Implementation of the Smith-Waterman algorithm.")
+ ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
+ (license (list license:gpl2 license:expat)))))
--
2.21.0
next prev parent reply other threads:[~2019-05-18 17:27 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2019-05-18 17:25 [bug#35792] [PATCH 0/7] Package freebayes Pierre Neidhardt
2019-05-18 17:26 ` [bug#35792] [PATCH 1/7] gnu: Add tabixpp Pierre Neidhardt
2019-05-18 17:26 ` Pierre Neidhardt [this message]
2019-08-08 14:30 ` [bug#35792] [PATCH 2/7] gnu: Add smithwaterman Ricardo Wurmus
2019-08-08 16:29 ` Efraim Flashner
2019-08-08 16:31 ` Ricardo Wurmus
2019-05-18 17:26 ` [bug#35792] [PATCH 3/7] gnu: Add multichoose Pierre Neidhardt
2019-05-18 17:26 ` [bug#35792] [PATCH 4/7] gnu: Add fsom Pierre Neidhardt
2019-05-18 17:26 ` [bug#35792] [PATCH 5/7] gnu: Add fastahack Pierre Neidhardt
2019-05-18 17:26 ` [bug#35792] [PATCH 6/7] gnu: Add vcflib Pierre Neidhardt
2019-05-18 17:26 ` [bug#35792] [PATCH 7/7] gnu: Add freebayes Pierre Neidhardt
2019-08-01 14:38 ` Pjotr Prins
2019-08-08 12:20 ` bug#35792: " Efraim Flashner
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